Re: Preventing rotation of a protein

From: Giacomo Fiorin (
Date: Thu Jul 18 2013 - 11:41:55 CDT

I think it boils down to whether you can assume that restraining the
orientation of the molecule carries a systematic error or not. If it does,
then applying the restraint to all the atoms of the molecule, or only to a
subset of it, won't fix the problem.

The ideal would be to use a cubic or truncated octahedral box, to
*not*apply any orientational restraint, and define instead all
variables in the rotated frame of the bigger molecule by using the
refPositionsGroup as in:

Then, of course, I do understand that it saves quite a few atoms with a
non-isotropic unit cell. See also Axel's reply that I just saw popping up.


On Thu, Jul 18, 2013 at 12:21 PM, Thomas Albers <>wrote:

> Hello!
> > Hello Thomas, the bias is only on the overall rotation, not on the
> internal
> > degrees of freedom: any force applied to the orientation colvar doesn't
> have
> > a projection along vectors that would change the internal structure of
> the
> > protein.
> Yes, but aren't the forces that are applied through the harmonic
> restrains acting only on the backbone?
> OK, one can argue that the random forces that cause the protein to
> diffuse away from its original orientation act only on the exterior,
> and the force applied to the backbone is of the same order of
> magnitude.
> I'm just slightly concerned that the colvar applies forces only to the
> backbone, and that might introduce systematic error.
> Regards,
> Thomas

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